cwl/preprocess/nonrefvcf/fixnonref-wf.cwl

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 cwlVersion: v1.0
   6 class: Workflow
   7 label: Scatter to fix VCF by removing GT fields that point to <NON_REF> and processing chrM
   8 requirements:
   9   ScatterFeatureRequirement: {}
  10 inputs:
  11   vcfdir:
  12     type: Directory
  13     label: Input VCF directory
  14
  15 outputs:
  16   fixedvcfs:
  17     type: File[]
  18     label: Fixed VCFs
  19     outputSource: fixnonref/fixedvcf
  20
  21 steps:
  22   getfiles:
  23     run: getfiles.cwl
  24     in:
  25       dir: vcfdir
  26     out: [vcfs]
  27   fixnonref:
  28     run: fixnonref.cwl
  29     scatter: [vcf]
  30     in:
  31       vcf: getfiles/vcfs
  32     out: [fixedvcf]